Rrn3 (RRN3 homolog, RNA polymerase I transcription factor) - Rat Genome Database

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Gene: Rrn3 (RRN3 homolog, RNA polymerase I transcription factor) Rattus norvegicus
Analyze
Symbol: Rrn3
Name: RRN3 homolog, RNA polymerase I transcription factor
RGD ID: 1305001
Description: Predicted to enable RNA polymerase I core binding activity; RNA polymerase I core promoter sequence-specific DNA binding activity; and RNA polymerase I general transcription initiation factor activity. Involved in positive regulation of neuron projection development. Predicted to be located in nucleolus. Predicted to be active in nucleus. Orthologous to several human genes including RRN3 (RRN3 homolog, RNA polymerase I transcription factor); PARTICIPATES IN mTOR signaling pathway; RNA polymerase I transcription pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100910121; LOC304714; RGD1305001; RNA polymerase I-specific transcription initiation factor RRN3; RNA polymerase I-specific transcription initiation factor RRN3-like; RRN3 RNA polymerase I transcription factor homolog; RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae); RRN3 RNA polymerase I transcription factor homolog (yeast); similar to AL023001 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8102,637,016 - 2,672,338 (-)NCBIGRCr8
mRatBN7.2102,129,949 - 2,165,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl102,129,978 - 2,165,663 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx106,826,708 - 6,861,997 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01033,703,845 - 33,739,134 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0102,033,162 - 2,067,849 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0103,170,387 - 3,214,648 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl103,170,742 - 3,214,655 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0102,057,042 - 2,092,164 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4101,492,181 - 1,527,197 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1101,492,186 - 1,543,048 (+)NCBI
Celera101,160,178 - 1,195,455 (-)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. RNA polymerase 1-driven transcription as a mediator of BDNF-induced neurite outgrowth. Gomes C, etal., J Biol Chem. 2011 Feb 11;286(6):4357-63. doi: 10.1074/jbc.M110.170134. Epub 2010 Nov 23.
3. TFIIB-related factors in RNA polymerase I transcription. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
4. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
Additional References at PubMed
PMID:8413268   PMID:12477932   PMID:15989966   PMID:18590050   PMID:22368283   PMID:28334682  


Genomics

Comparative Map Data
Rrn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8102,637,016 - 2,672,338 (-)NCBIGRCr8
mRatBN7.2102,129,949 - 2,165,381 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl102,129,978 - 2,165,663 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx106,826,708 - 6,861,997 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01033,703,845 - 33,739,134 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0102,033,162 - 2,067,849 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0103,170,387 - 3,214,648 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl103,170,742 - 3,214,655 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0102,057,042 - 2,092,164 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4101,492,181 - 1,527,197 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1101,492,186 - 1,543,048 (+)NCBI
Celera101,160,178 - 1,195,455 (-)NCBICelera
Cytogenetic Map10q11NCBI
RRN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381615,060,022 - 15,094,335 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1615,060,033 - 15,094,311 (-)EnsemblGRCh38hg38GRCh38
GRCh371615,153,879 - 15,188,192 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361615,061,380 - 15,095,659 (-)NCBINCBI36Build 36hg18NCBI36
Build 341615,061,379 - 15,095,613NCBI
Celera1616,150,521 - 16,184,795 (+)NCBICelera
Cytogenetic Map16p13.11NCBI
HuRef1614,799,197 - 14,833,480 (-)NCBIHuRef
CHM1_11615,095,601 - 15,129,884 (+)NCBICHM1_1
T2T-CHM13v2.01615,061,074 - 15,095,386 (-)NCBIT2T-CHM13v2.0
Rrn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391613,598,563 - 13,632,705 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1613,598,572 - 13,632,703 (+)EnsemblGRCm39 Ensembl
GRCm381613,780,699 - 13,814,841 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1613,780,708 - 13,814,839 (+)EnsemblGRCm38mm10GRCm38
MGSCv371613,780,792 - 13,814,934 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361613,694,277 - 13,728,419 (+)NCBIMGSCv36mm8
Celera1614,384,965 - 14,419,116 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map169.59NCBI
Rrn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955442129,106 - 166,258 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955442129,106 - 166,258 (+)NCBIChiLan1.0ChiLan1.0
RRN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21815,272,893 - 15,309,408 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11619,055,740 - 19,092,270 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01613,664,478 - 13,700,942 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RRN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1628,478,770 - 28,507,722 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl628,478,829 - 28,507,696 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha629,841,964 - 29,870,919 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0628,641,773 - 28,670,927 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl628,641,780 - 28,670,894 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1628,444,804 - 28,473,963 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0628,334,911 - 28,364,048 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0628,740,669 - 28,769,347 (-)NCBIUU_Cfam_GSD_1.0
Rrn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344114,795,421 - 114,828,934 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365012,893,298 - 2,926,804 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365012,893,304 - 2,926,795 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RRN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl37,537,133 - 7,571,992 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.137,537,131 - 7,571,990 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RRN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1514,235,368 - 14,271,790 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl514,235,414 - 14,272,020 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606815,775,231 - 15,812,052 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rrn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248248,582,803 - 8,614,313 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248248,582,754 - 8,615,073 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rrn3
266 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000004459
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat

Markers in Region
D10Got407  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2102,143,656 - 2,143,823 (-)MAPPERmRatBN7.2
Rnor_6.0103,200,770 - 3,200,934NCBIRnor6.0
Rnor_6.0103,176,930 - 3,177,094NCBIRnor6.0
Rnor_5.0102,054,626 - 2,054,790UniSTSRnor5.0
Rnor_5.0102,078,286 - 2,078,450UniSTSRnor5.0
RGSC_v3.4101,513,283 - 1,513,447UniSTSRGSC3.4
Celera101,173,877 - 1,174,041UniSTS
Cytogenetic Map10q11UniSTS
RH130091  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2102,130,069 - 2,130,256 (+)MAPPERmRatBN7.2
mRatBN7.2102,130,069 - 2,130,256 (-)MAPPERmRatBN7.2
Rnor_6.0101,689,720 - 1,689,906NCBIRnor6.0
Rnor_6.0103,214,348 - 3,214,534NCBIRnor6.0
Rnor_5.010579,272 - 579,458UniSTSRnor5.0
Rnor_5.0102,091,864 - 2,092,050UniSTSRnor5.0
RGSC_v3.4101,526,898 - 1,527,084UniSTSRGSC3.4
Celera101,160,291 - 1,160,477UniSTS
Cytogenetic Map10q11UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 37 11 8
Low 4
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000004459   ⟹   ENSRNOP00000004459
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl103,170,777 - 3,214,647 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082082   ⟹   ENSRNOP00000074735
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl102,129,978 - 2,165,663 (-)Ensembl
Rnor_6.0 Ensembl103,179,346 - 3,214,647 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl103,179,437 - 3,180,813 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093528   ⟹   ENSRNOP00000076210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl103,170,742 - 3,214,655 (+)Ensembl
RefSeq Acc Id: NM_001135846   ⟹   NP_001129318
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8102,637,017 - 2,672,295 (-)NCBI
mRatBN7.2102,129,957 - 2,165,241 (-)NCBI
Rnor_6.0103,179,346 - 3,214,647 (+)NCBI
Rnor_5.0102,057,042 - 2,092,164 (+)NCBI
RGSC_v3.4101,492,181 - 1,527,197 (+)RGD
Celera101,160,178 - 1,195,455 (-)RGD
Sequence:
RefSeq Acc Id: XM_008767458   ⟹   XP_008765680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8102,637,016 - 2,672,338 (-)NCBI
mRatBN7.2102,129,949 - 2,165,381 (-)NCBI
Rnor_6.0103,170,387 - 3,214,648 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129318 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765680 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66485 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074735
  ENSRNOP00000074735.2
RefSeq Acc Id: NP_001129318   ⟸   NM_001135846
- UniProtKB: B2GV13 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765680   ⟸   XM_008767458
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8U0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074735   ⟸   ENSRNOT00000082082
RefSeq Acc Id: ENSRNOP00000004459   ⟸   ENSRNOT00000004459
RefSeq Acc Id: ENSRNOP00000076210   ⟸   ENSRNOT00000093528

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GV13-F1-model_v2 AlphaFold B2GV13 1-661 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305001 AgrOrtholog
BioCyc Gene G2FUF-26207 BioCyc
Ensembl Genes ENSRNOG00000003326 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082082.3 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099831 IMAGE-MGC_LOAD
InterPro RNA_pol_I_trans_ini_fac_RRN3 UniProtKB/TrEMBL
KEGG Report rno:304714 UniProtKB/TrEMBL
MGC_CLONE MGC:187970 IMAGE-MGC_LOAD
NCBI Gene 304714 ENTREZGENE
PANTHER RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3-RELATED UniProtKB/TrEMBL
  RNApolI_tif_RRN3 UniProtKB/TrEMBL
Pfam RRN3 UniProtKB/TrEMBL
PhenoGen Rrn3 PhenoGen
RatGTEx ENSRNOG00000003326 RatGTEx
UniProt A0A0G2K8U0 ENTREZGENE, UniProtKB/TrEMBL
  B2GV13 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rrn3  RRN3 homolog, RNA polymerase I transcription factor  LOC100910121  RNA polymerase I-specific transcription initiation factor RRN3-like  Data merged from RGD:6500155 737654 PROVISIONAL
2015-07-30 Rrn3  RRN3 homolog, RNA polymerase I transcription factor  Rrn3  RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910121  RNA polymerase I-specific transcription initiation factor RRN3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-30 Rrn3  RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)  Rrn3  RRN3 RNA polymerase I transcription factor homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Rrn3  RRN3 RNA polymerase I transcription factor homolog (yeast)  RGD1305001_predicted  similar to AL023001 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1305001_predicted  similar to AL023001 protein (predicted)  LOC304714_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC304714_predicted  similar to AL023001 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL